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lib/Bio/Cluster/UniGene.pm  view on Meta::CPAN

 Usage   : used by ClusterIO
 Returns : a new Bio::Cluster::Unigene object

=cut

sub new {
    # standard new call..
    my($caller,@args) = @_;
    my $self = $caller->SUPER::new(@args);

    my ($ugid,$desc,$mems,$size,$species,$dispid,$id,$ns,$auth,$v,$seqfact) =
	$self->_rearrange([qw(UNIGENE_ID
			      DESCRIPTION
			      MEMBERS
			      SIZE
			      SPECIES
			      DISPLAY_ID
			      OBJECT_ID
			      NAMESPACE
			      AUTHORITY
			      VERSION
			      SEQFACTORY
			      )], @args);

    $self->{'_alphabet'} = 'dna';

    $self->unigene_id($ugid) if $ugid;
    $self->description($desc) if $desc;
    $self->sequences($mems) if $mems;
    $self->size($size) if defined($size);
    $self->display_id($dispid) if $dispid; # overwrites ugid
    $self->object_id($id) if $id;          # overwrites dispid
    $self->namespace($ns || 'UniGene');
    $self->authority($auth || 'NCBI');
    $self->version($v) if defined($v);
    if( ! defined $seqfact ) {
	$seqfact = Bio::Seq::SeqFactory->new
	    (-verbose => $self->verbose(),
	     -type => 'Bio::Seq::RichSeq');
    }
    $self->sequence_factory($seqfact);